<!--
 * SystemsInfluenza.org Website v2.0
 * Copyright(c) 2006-2012 Institute for Systems Biology, Seattle, Washington, USA
 * codefor@systemsbiology.org
 * http://www.gnu.org/licenses/lgpl.html
 * Author: Hector Rovira
-->
<html>
<head>
    <link rel="stylesheet" type="text/css" href="http://extjs.cachefly.net/ext-3.4.0/resources/css/ext-all.css">
    <link rel="stylesheet" type="text/css" href="http://extjs.cachefly.net/ext-3.4.0/resources/css/xtheme-gray.css"/>
    <link rel="stylesheet" type="text/css" href="css/stylesheet.css"/>

    <script type="text/javascript" src="http://extjs.cachefly.net/ext-3.4.0/adapter/ext/ext-base.js"></script>
    <script type="text/javascript" src="http://extjs.cachefly.net/ext-3.4.0/ext-all.js"></script>

    <script type="text/javascript" src="js/analytics.js"></script>
    <script type="text/javascript" src="js/data_grid.js"></script>
    <script type="text/javascript" src="js/annotations_grid.js"></script>

    <script type="text/javascript">
        var annotations_grid_WholeLung = {};
        var annotations_grid_SILAC = {};
        var agconfig = { width: 900, height: 300 };
    </script>
    <script type="text/javascript" src="/repositories/datasets/contents/Immune-response-to-infection/WholeLung12h/annotations_grid.json"></script>
    <script type="text/javascript" src="/repositories/datasets/contents/Immune-response-to-infection/SILAC/annotations_grid.json"></script>

    <script type="text/javascript">
        Ext.onReady(function() {
            new AnnotationsGrid("c_WholeLung12h", annotations_grid_WholeLung, agconfig);
            new AnnotationsGrid("c_SILAC", annotations_grid_SILAC, agconfig);

            new DataGrid("c_Pilot_Eicosanoids_Data_1",
                    "/repositories/datasets/query/Immune-response-to-infection/Pilot_Eicosanoids_Data_1.tsv",
                    ["Infection Agent", "Days post-infection"], agconfig);
            new DataGrid("c_Pilot_Eicosanoids_Data_2",
                    "/repositories/datasets/query/Immune-response-to-infection/Pilot_Eicosanoids_Data_2.tsv",
                    ["Infection Agent", "Days post-infection"], agconfig);
            new DataGrid("c_Pilot_Eicosanoids_Data_3",
                    "/repositories/datasets/query/Immune-response-to-infection/Pilot_Eicosanoids_Data_3.tsv",
                    ["Infection Agent", "Days post-infection"], agconfig);
        });
    </script>
</head>
<body>
<div class="pagetitle">Immune Response to Infection</div>

<div class="text">
    This portion of the program is focused on understanding differences in host response triggered in vivo by influenza
    infections of varying pathogenicity. Our model system employs three <a href="#" onclick="window.parent.contentPanel.activate('viral_models'); return false;">mouse-adapted strains</a> of
    influenza that differ only in their hemagglutinin (HA) and neuraminidase (NA) surface proteins yet span a wide range
    in LD50.
</div>
<div class="text">
    The majority of our work on the innate response to infection in vivo focuses on events that occur during the first
    24 hours in order to distinguish critical host-virus interactions from non-specific responses to stress or tissue
    damage. This approach presents significant challenges to transcriptome analysis due to the relatively small number
    of cells that are infected and the consequent dilution of infection-induced gene expression changes. By combining
    data from exon microarrays and a microfluidic-based real-time qPCR platform, we are comprehensively characterizing
    the host responses in both the lung and trachea with high temporal resolution. In parallel, samples are collected
    from the same mice for proteomic, lipidomic, and histological analyses. By integrating data from all of these
    approaches, we are developing a systems-level model of the innate response to influenza infection.
</div>

<div class="text">
    <h3>Exon Microarray Data</h3>
    <strong>Affymetrix GeneChip Mouse Exon 1.0 ST Arrays of Mouse Lung</strong><br/>
    C57BL/6J mice were infected with the described strains and euthanized at the time points indicated below. Tissues
    were then harvested and RNA was extracted using TRIzol. Samples were amplified and hybridized to Affymetrix GeneChip
    Mouse Exon 1.0 ST Arrays.
    <div id="c_WholeLung12h"></div>
</div>

<div class="text">
    <h3>SILAC Proteomics Data</h3>
    Stable isotope labeling with amino acids in cell culture (SILAC) is a technique that provides a means by which to
    mix two protein samples together (e.g. infected and uninfected) with the goal of being able to discriminate
    differences between the two. SILAC labeling of one of the two samples is accomplished by incorporating
    "heavy"-labeled amino acids during protein synthesis. When analyzed by mass spectrometry, the SILAC-labeled proteins
    display a mass shift compared to their unlabeled ("light") counterparts in the other sample, thereby providing means
    to identify differences for individual proteins in both samples. This approach has been extended to in vivo studies
    here by feeding mice a diet containing 13C6 lysine.
    <br/>
    <br/>
    In this dataset, C57BL/6J mice received either 105 PFU of influenza virus PR8 or mock PBS intranasally. 18 hours
    after infection, mice were euthanized, perfused, and lung tissue was collected ("light" labeling). Lung tissue from
    uninfected SILAC mice was processed in parallel ("heavy" labeling). Subsequently, the tissues were homogenized,
    mixed according to the scheme below, fractionated, in-gel digested with LysC, and run on a LTQ-Orbitrap
    mass-spectrometer.

    <dl><b>Sample Schemes</b>
        <dt>Sample 1</dt>
        <dd>1:1 mix of lung tissue from a PR8-infected mouse (light labeling) with lung tissue from an
            uninfected mouse (heavy labeling)
        </dd>
        <dt>Sample 2</dt>
        <dd>1:1 mix of lung tissue from an uninfected mouse (light labeling) with lung tissue from an uninfected
            mouse (heavy labeling)
        </dd>
    </dl>
    <div id="c_SILAC"></div>
</div>

<div class="text">
    <h3>Eicosanoids (Lipidomics Core A) Data</h3>
    C57BL/6J mice were infected with a sublethal dose of PR8 on day 0. Brocho alveolar lavage (BAL) fluid was extracted
    on designated days post-infection. Eicosanoids were measured in BALF quantitatively using mass spectrometry.
    <br/>
    <br/>
    <div class="experiment_label">EXPERIMENT 10-06-09</div>
    <div class="subtitle">Values are expressed in pmol/ml of lavage</div>
    <div id="c_Pilot_Eicosanoids_Data_1"></div>

    <br/>
    <div class="experiment_label">EXPERIMENT 02-23-10</div>
    <div class="subtitle">Values are expressed in pmol/ml of lavage</div>
    <div id="c_Pilot_Eicosanoids_Data_2"></div>

    <br/>
    <div class="experiment_label">EXPERIMENT 04-01-11</div>
    C57BL/6J mice were infected with a sublethal dose of X31, PR8, or lethal dose of PR8 (2x10^5 PFU) on day 0. Brocho alveolar lavage fluid (BALF) was extracted on designated days post-infection. Eicosanoids were measured in BALF quantitatively using mass spectrometry.
    <div class="subtitle">Values are expressed in pmol/ml of lavage</div>
    <div id="c_Pilot_Eicosanoids_Data_3"></div>
</div>
</body>
</html>